1 Introduction

Hi, welcome to this very first lesson of the “Introduction to the EpiGraphHub Platform” course.

This lesson will give you a general overview of the EpiGraphHub, so that you get familiar with the platform, get ready for the exciting lessons coming next in this course, and eventually get the most of the EpiGraphHub to make sense of all the great health-related data you have at hand.

2 Learning Objectives

By the end of this lesson,

3 What is the EpiGraphHub platform?

The EpiGraphHub is a web platform that:

You can access the EpiGraphHub through your web browser at this address: https://epigraphhub.org/superset/welcome/

In addition to providing a centralized access to the datasets, it allows users to:

  1. make exploratory analyses directly on the platform,
  2. create dynamic charts,
  3. build online dashboards that can be shared with colleagues without prior knowledge of a programming language.

In the next lessons, we will focus on the possibilities of our platform for non-programmer users.

3.1 Access to the EpiGraphHub Platform

Let’s get started and go on the platform together. In the address bar of your web browser, type the address: https://epigraphhub.org/superset/welcome/ and press Enter.

You will land on the Welcome page below.

Anyone can log in using the guest username and password. However, I recommend you create an account to have access to more functionalities of our platform.

3.1.1 Create a new account

To create an account, click on the button SIGN UP highlighted below.

The page below will open. You need to fill the fields with your information and click on the SAVE button to create an account.

You will then receive an email that requests you to activate your user, by following a link.

3.1.2 Log in to the platform

Once you have signed up and activated your user, click on the Login icon.

A new page will then appear, asking for your USERNAME and PASSWORD. In these fields, enter the username and password of the account you have just created, and press the button SIGN IN to log in to the platform.

If you did not create an account, use the guest account:

  • USERNAME: guest
  • PASSWORD: guest

When logged in, you will arrive on the following Home page:

At the top of the page, you can see the Menu bar. In what follows, we will go through the different menus together.

3.2 Dashboards

First, we will explore the Dashboards menu by selecting the Dashboards icon:

This is what you will see when the Dashboards page opens:

Here, you will find all the dashboards created and published on our platform.

In the first rectangle highlighted, you can apply some filters to search over all dashboards. Below, an explanation of each field:

  • OWNER: In this field, you can select the owner of the dashboard. He is the user (or users) allowed to edit it.
  • CREATED BY: In this field, you can select the user that created the dashboard.
  • STATUS: In this field, you can select if the dashboard is published or just a draft. If you select the draft option, you will just see the draft dashboards created by your user.
  • FAVORITE: In this field, you can select the dashboards favored by your user.
  • CERTIFIED: In this field, you can select the approved dashboards.
  • SEARCH: In this field, you can search by the title of the dashboard.

In the second rectangle, you can also see when the last modification of the dashboard was done (Modified) and who did it (Modified by).

In the next lessons of this course, you will learn how to create such dashboards. For now, let’s already have a look at one example of a dashboard, the COVID-19 Switzerland.

To open the dashboad, just click on its name. If you don’t see it, search for it by typing its name in the SEARCH field and pressing ENTER.

After clicking on the name of the dashboard, the window below will open:

This dashboard is made of 6 panels:

  • a description box
  • a filter-box chart (Canton Selector panel),
  • a country-map chart, and
  • three time-series charts

In the Selector box highlighted in the following figure, you can select the time range you are interested in (e.g., last quarter, last year), change the time grain (e.g., weekly, daily granularity), and select one or several cantons. The cantons selected in this box will be used to make all the Charts of the dashboard.

You can also temporarily hide some canton by double-clicking on it in the legend above the plot, and change the time range using the sliding window below the plot.

If you click on the three dots highlighted below, you will see some options that allow you to download the dashboard as an image, share the dashboard, open it on full screen or save it with another name as a copy.

3.3 Charts

Now let’s explore the Charts menu by selecting the Charts icon:

When the Charts page opens, you will see a list of the different charts that were saved.

In the first rectangle highlighted, you can apply some filters to search over the charts. Below, an explanation of each field:

  • OWNER: In this field, you can select the owner of the chart. He is the user (or users) allowed to edit it.
  • CREATED BY: In this field, you can select the user that created the chart.
  • CHART TYPE: In this field, you can select a specific type of chart.
  • DATASET: In this field, you can select the dataset used to make the chart.
  • FAVORITE: In this field, you can select the charts favored by your user.
  • CERTIFIED: In this field, you can select the approved charts.
  • SEARCH: In this field, you can search by the title of the chart.

In the second rectangle, you can also see when the last modification of the chart was done (Last modified) and who did it (Modified by).

To look at one chart, click on its name. Let’s have a look at the chart, entitled: Evolution of weekly COVID hospitalisations in Switzerland by Canton. To do so, type this title in the SEARCH field, press ENTER, and click on the name highlighted in the figure below.

The Explore page below will show on your screen:

To increase the size of the plot, click on the symbol highlighted in the figure above.

We can save and share this chart in different ways. The different options are highlighted in the figure above.

Let’s understand the meaning of each icon represented below:

  1. Selecting this icon, you get a link to share the chart.
  2. Selecting this icon, you can share the link of the chart by email.
  3. Selecting this icon, you get the html embed code to use the chart in other web applications.
  4. Selecting this icon, you get the data used to make the chart in the .json format.
  5. Selecting this icon, you get the data used to make the chart in the .csv format.
  6. Selecting this icon, you will see the following options:

  • The Edit properties option is restricted to the owner of the chart.
  • The View query option allows you to get the SQL code used to filter the data used to make the plot.
  • The Run in SQL Lab option it’s not working in the guest account (this account don’t have the access to make SQL queries).
  • The Download as image allows you to download the chart as an image.

In the next lessons, you will also learn how to create this kind of chart and get familiar with the Explore page, which has other features such as:

  1. See the current dataset (here switzerland.foph_hosp_d) used to create the chart and the list of Columns in the dataset.
  2. Choose the visualisation type you want, specify the time range and granularity (e.g., daily, weekly) of interest, and define the query that will be used to build your chart.
  3. Visualise the resulting chart and data generated by the query.

3.4 Databases and datasets

Now let’s explore the Data menu by selecting the Data icon:

When you click on the Data menu, you can see these two options: Databases and Datasets.

It’s essential to highlight the difference between the databases and the datasets:

  • A Dataset contains information organized as a table with different rows and columns.
  • While the Database is an ensemble of multiple datasets according to some criteria.

Moreover, as you can already notice in the figure above, datasets within a database are organised into Schemas, as we will see further below.

3.4.1 Databases

If you click on Databases, you will see the following databases:

  • The epigraphhub database. It is the database where our validated public data is maintained. It contains exclusively public domain data, either generated internally by the project or integrated from other sources. It can be read by all users but only EpiGraphHub analysts can write to it, creating or updating tables.

  • The Sandbox database. It is the database that EpiGraphHub analysts use to maintain temporary datasets for testing purposes. Any user has read and write privileges on it but no dataset is guaranteed to be persisted for long periods of time.

  • The Google sheets is a database that will be used when accessing data stored in a Google spreadsheets. We will see in the next chapter how to import such data.

3.4.2 Datasets

If you now select the Datasets option, you will see the list of datasets available on the platform.

In the first rectangle highlighted, you can apply some filters to search over the datasets. Below there is an explanation of each field:

  • OWNER: In this field, you can select the owner of the dataset. He is the user (or users) allowed to edit it.

  • DATABASE: The database where the dataset is stored.

  • SCHEMA: is a sub-level of organization of the database. You can think of the database as a folder on your computer and the schemas being the subfolders.

  • TYPE: It determines how the table is stored in the database. If Physical, it means that the table is saved in the original database. If virtual, it means that the table is saved in the metadata bank of the superset.

  • SEARCH: In this field, you can search by the title of the dataset.

In the second rectangle, you also can see when the last modification of the dataset was done (Modified) and who did it (Modified by).

To organise our data, the datasets related to a specific country are saved in the schema named like the country. For example, the datasets available for Switzerland, are saved in the schema switzerland.

Datasets that are not specific to a single country, and have data related to the whole world are saved in the schema public.

You can see a complete list of the datasets available on the platform with a summary of their content in the platform documentation.

When you choose a database and a schema, you will see the list of datasets available for these configurations. For example, if you select DATABASE equal epigraphhub and SCHEMA equal switzerland, you will see the following datasets:

Congratulations! You reached the end of this first lesson, which introduced you to the EpiGraphHub.

Hopefully, you are now familiar with the platform, and have a good idea of the type of charts and dashboards that you will be able to easily build. By now, you should also know the different databases available on EpigraphHub and be clear about some key concepts like the difference between a database and a dataset.


In the next lesson, you will actually start exploring your first dataset. See you there :)

Contributors

The following team members contributed to this lesson:

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